3D4U

Bovine thrombin-activatable fibrinolysis inhibitor (TAFIa) in complex with tick-derived carboxypeptidase inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of activated thrombin-activatable fibrinolysis inhibitor, a molecular link between coagulation and fibrinolysis.

Sanglas, L.Valnickova, Z.Arolas, J.L.Pallares, I.Guevara, T.Sola, M.Kristensen, T.Enghild, J.J.Aviles, F.X.Gomis-Ruth, F.X.

(2008) Mol Cell 31: 598-606

  • DOI: https://doi.org/10.1016/j.molcel.2008.05.031
  • Primary Citation of Related Structures:  
    3D4U

  • PubMed Abstract: 

    Thrombin-activatable fibrinolysis inhibitor (TAFI) is a metallocarboxypeptidase (MCP) that links blood coagulation and fibrinolysis. TAFI hampers fibrin-clot lysis and is a pharmacological target for the treatment of thrombotic conditions. TAFI is transformed through removal of its prodomain by thrombin-thrombomodulin into TAFIa, which is intrinsically unstable and has a short half-life in vivo. Here we show that purified bovine TAFI activated in the presence of a proteinaceous inhibitor renders a stable enzyme-inhibitor complex. Its crystal structure reveals that TAFIa conforms to the alpha/beta-hydrolase fold of MCPs and displays two unique flexible loops on the molecular surface, accounting for structural instability and susceptibility to proteolysis. In addition, point mutations reported to enhance protein stability in vivo are mainly located in the first loop and in another surface region, which is a potential heparin-binding site. The protein inhibitor contacts both the TAFIa active site and an exosite, thus contributing to high inhibitory efficiency.


  • Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular (Facultat de Ciències), Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase B2309Bos taurusMutation(s): 0 
EC: 3.4.17.20
UniProt
Find proteins for Q2KIG3 (Bos taurus)
Explore Q2KIG3 
Go to UniProtKB:  Q2KIG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2KIG3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Carboxypeptidase inhibitor74Rhipicephalus bursaMutation(s): 0 
UniProt
Find proteins for Q5EPH2 (Rhipicephalus bursa)
Explore Q5EPH2 
Go to UniProtKB:  Q5EPH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5EPH2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.171 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.156 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.2α = 90
b = 84.2β = 90
c = 127.9γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary